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6 protocols using anti v5

1

Investigating MYC-interacting proteins using affinity purification

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Cycloheximide and MG132 were purchased from Cayman Chemical (Ann Arbor, MI, USA). Lithium chloride was obtained from Thermo Fisher Scientific (Waltham, MA, USA). S-protein agarose beads were obtained from Merck (Rahway, NJ, USA). MYC antibody-conjugated agarose beads were from Thermo Fisher Scientific (Waltham, MA, USA). The following antibodies were used: anti-FLAG (Proteintech; San Diego, CA, USA), anti-MYC (Proteintech; San Diego, CA, USA), anti-OTUD7B (Proteintech; San Diego, CA, USA), anti-cyclophilin B (Invitrogen; Waltham, MA, USA), anti-HSP90 (Santa Cruz Biotechnology; Santa Cruz, CA, USA), anti-HA (Santa Cruz Biotechnology; Santa Cruz, CA, USA), anti-V5 (Proteintech; San Diego, CA, USA), anti-α-tubulin (Proteintech; San Diego, CA, USA), and anti-lamin B1 (Santa Cruz Biotechnology; Santa Cruz, CA, USA).
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2

Antibody Validation and ER Stress Assays

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Anti-V5, FLAG and GAPDH antibodies were purchased from Proteintech. Anti-α-Tubulin and anti-HA antibodies were purchased from Sigma. Anti-Sox2, Nanog and Oct4 antibodies were purchased from Abcam. The following antibodies were used: anti-FKBP9 (Invitrogen), anti-Calnexin (Santa Cruz), anti-Nestin (R&D Systems), anti-pmTOR (Invitrogen), anti-pP70S6K (Millipore), anti-pERK1/2 (Promega), anti-p65 (EPITOMICS), anti-ASK1 (Santa Cruz), anti-pASK1 (Santa Cruz), anti-pIRE1α (NOVUS). Other antibodies for immunoblotting were purchased from Cell Signaling Technology. Aggresome Detection Kit was purchased from Abcam. Thapsigargin (Tg) and tunicamycin (Tm) were purchased from Apexbio. Proteasome inhibitor MG132 and lysosomal inhibitors Bafalomycin A1 (Baf A1) and chloroquine (CQ) were obtained from Sigma. Drugs were dissolved and stored at − 20 °C or − 80 °C according to the instructions.
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3

TLR-Mediated Signaling Pathway Analysis

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Lipopolysaccharide (LPS, E. coli 0111: B4, TLR4 ligand), poly(I:C) (TLR3 ligand), and CpG ODN (TLR9 ligand) were purchased from Sigma-Aldrich. ChIP Grade Protein G Magnetic Beads, Cell Lysis Buffer, Anti-Myd88, Anti-Traf6, Anti-p65, Anti-p-p65 (Ser536), Anti-Ikkα/β, Anti-p-Ikkα/β (S176/180), Anti-IκBα, Anti-p-IκBα (S32), Anti-ERK, Anti-p-ERK (Thr202-Tyr204), Anti-JNK, Anti-p-JNK (Thr183-Tyr185), Anti-p38, Anti-p-p38 (Thr180-Tyr182) and Anti-Syk and Anti-p-Syk (Tyr-525/526) were from Cell Signaling Technology. Anti-DAP12 was purchased from Abcam. Anti-β-actin, Anti-rabbit IgG-HRP, and anti-mouse IgG-HRP were from Santa Cruz Biotechnology. Anti-LaminA/C, Anti-Flag and Anti-Myc and Anti-V5 were purchased from Proteintech. Anti-Ocilrp2 (AF3370) was from purchased R&D. The NF-κB inhibitor BAY11-7082 (10 μM), Tbk inhibitor Amlexanox (10 μM), Mek inhibitor PD98059 (10 μM), PI3K inhibitor Wortmannin (5 μM), Erk inhibitor SHC772984 (10 μM), Jnk inhibitor SP600125 (10 μM), or p38 inhibitor SB203580 (10 μM), Syk inhibitor R406 (5 μM) were from Selleckchem.
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4

Investigating GNIP1 Regulation of Autophagy

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GNIP1/RNF90 (Abcam; ab170538), β-Actin (Proteintech; 66,009–1-lg), GAPDH (OriGene; TA802519), DDDDK Tag (Proteintech; 20,543-1-AP), LC3B (Proteintech; 18,725–1-AP), SQSTM1/p62 (Proteintech; TA502127), BECN1 (Proteintech; 11,306–1-AP), ULK1 (Cell Signaling Technology; 6439), HA-tag (Thermo Fisher Scientific; 26,183), GFP (Proteintech; 66,002-1-lg), UB antibody (Proteintech; 10,201–2-AP), K48 (Cell Signaling Technology; 8081), K63 (Cell Signaling Technology; 5621), PIK3C3/VPS34 (Thermo Fisher Scientific; PA5-35,215), 14–3-3ζ (Proteintech; 14,881-1-AP), anti-His (Proteintech; 10,001-0-AP/ 66,005-1-LG), anti-V5 (Proteintech; 14,440-1-AP). Cycloheximide (Sigma; C7698), DMSO (Sigma; D2650), MG132 (Biovision; 1791-5). Myc-DDDK-Tag-GNIP1, pcDNA3.1-Flag-GNIP1-W57A, PCDH-Flag-GNIP1, pEGFP-C2-LC3B, pCMV-HA-BECN1, pCMV-HA, pcDNA3.1-Flag-PIK3C3, pCMV-Flag-14-3-3ζ, pcDNA3.1-V5-BBCC, pcDNA3.1-V5-His-RBB and pcDNA3.1-V5-His-CCB plasmids were constructed by ourselves.
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5

Western Blot Analysis of Protein Targets

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Total protein extracts were obtained using the RIPA lysis buffer (Sigma, USA). Protein concentration was measured using a BCA Protein Assay kit (Pierce, USA). Protein samples were resolved in 7.5 and 15% SDS-PAGE gels and transferred to Immuno-blot PVDF Membrane (Bio-Rad, USA). The membranes were blocked using 5% non-fat milk in Tris-buffered saline with Tween-20. The membranes were then incubated with primary antibodies followed by incubation with secondary peroxidase labeled anti-rabbit or anti-mouse antibodies (Santa Cruz Biotechnology, USA). The protein signals were detected using an enhanced chemiluminescent solution (Millipore, USA). Primary antibodies used include anti-tubulin, anti-actin (Sigma, USA), anti-PFKP, anti-p53, anti-phospho-p53, anti-p21, anti-ACC, anti-phospho-ACC, anti-AMPK, anti-phospho-AMPK (Cell Signaling Technology, USA), anti-PFKM, anti-PFKL, anti-GLUT1 and anti-V5 (Proteintech Group, USA).
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6

Antibody Sources for Protein Analysis

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Anti-HA, anti-DYKDDDDK, anti-Myc, and anti-His antibodies were provided by Cell Signaling Technology (CST, Danvers, MA, USA), while Santa Cruz Biotechnology (Dallas, TX, USA) was the source of the anti-USP48 antibody. The anti-USP48, anti-HMGA2, anti-Tubulin and anti-V5 antibodies were supplied by Proteintech (Wuhan), and the PTM BioLab (Hanzhou, China) provided the anti-Ub antibody. Anti-c-Myc, anti-His, and Anti-HA agarose beads were supplied by Medchem Express (MCE) based in NJ, USA. 2-D08, MG132 and CQ were provided by SelleckChem located in Houston, TX, USA.
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